plot_h: Plot function for estimated hybrid indices and credible...

In ribailey/gghybrid: Evolutionary Analysis of Hybrids and Hybrid Zones

Plot function for estimated hybrid indices and credible intervals.

Description

Plot function for estimated hybrid indices and credible intervals.

Usage

plot_h(
  data,
  test.subject = "INDLABEL",
  POPID.name = "POPID",
  mean.h.by = NULL,
  sort.by = "h_posterior_mode",
  col.group = NULL,
  group.sep = NULL,
  fill.source = FALSE,
  basic.lines = TRUE,
  source.col = NULL,
  source.limits = NULL,
  custom.abline = NULL,
  ...
)

Arguments

data	Name of an hi object produced by the esth function.
test.subject	test.subject object from esth. Default “INDLABEL”.
POPID.name	Character string. Name of the designated POPID field. Default “POPID”, but this is ignored if there is no POPID field.
mean.h.by	Character string. Calculate mean hybrid index by group for the group designations in this field. Creates a column called ‘mean_h’ for ordering data points on the figure using sort.by.
sort.by	Character vector. Fields by which to sort the test subjects by value along the x axis in the figure. Can include ‘mean_h’. Default is ‘h_posterior_mode’.
col.group	Character string. Variable by which to group colouring of data points.
group.sep	Character string. Variable by which to separate groups of data points with vertical grey lines in the plot.
fill.source	Logical. Whether to fill the area of the plot representing parental reference samples with a grey background. Default FALSE.
basic.lines	Logical. If TRUE, adds horizontal grey dashed lines at hybrid index 0, 0.5 and 1. Default TRUE.
source.col	Character vector. Colours to be used for the two parental reference set data points.
source.limits	Character vector. Colours of horizontal dashed lines marking the innermost credible interval for each parental reference set. Used to indicate whether test subjects are clearly outside the hybrid index ranges of parentals.
custom.abline	An abline of the user's choosing.
...	Further graphical parameters.

Value

Alongside the plot, returns a data.table and data.frame useful for creating a legend, with the specified test.subject field, the mean.h.by field if specified, along with the mean_h value, the Source field, the colours in a field named col.Dark2, and the row number for ordering in field rn.

Author(s)

Richard Ian Bailey [e-mail]

Examples

## Not run: 
abc = plot_h(data=hindlabel$hi,
test.subject=hindlabel$test.subject,
mean.h.by="POPID",			                    #Calculate the mean hybrid index for each value of the "POPID" column#
sort.by=c("mean_h","POPID","h_posterior_mode"),	#Order test subjects along the x axis by the mean hybrid index calculated above and also by 
						                         #individual hybrid index ("POPID" is included as some population pairs may have identical mean hi).
col.group="POPID",
group.sep="POPID",
fill.source=TRUE,
basic.lines=FALSE,
source.col=c("blue","red"),
source.limits=c("blue","red"),
custom.abline=abline(h=0.75,col="magenta",lwd=2),
cex=1,pch=16,
cex.lab=1.5,cex.main=1.5,ylim=c(0,1))

#Adding a legend with base R's "legend" function, using the plot_h object created above, "abc":
setkey(abc,rn);		#Order data by row number#
legend("topleft",	#Place the legend in the top left of the figure#
abc[,POPID], 		#Name of the field by which data point colours are grouped#
bg="white",			#Background colour#
text.col=c("black"), #Text colour#
pch=22, 				#Text size#
col=abc[,col.Dark2], #Name of the field containing colour information#
pt.bg=abc[,col.Dark2],	#Name of the field containing colour information#
ncol=4,				#Number of columns for splitting the group names#
cex=0.6, pt.cex=0.7)

## End(Not run)

ribailey/gghybrid documentation built on Feb. 2, 2024, 12:53 a.m.